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ncbi / amr

AMRFinderPlus - Identify AMR genes and point mutations, and virulence and stress resistance genes in assembled bacterial nucleotide and protein sequence.
https://www.ncbi.nlm.nih.gov/pathogens/antimicrobial-resistance/AMRFinder/
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Use the program on Viruses ? #88

Open conchaeloko opened 2 years ago

conchaeloko commented 2 years ago

Hi, First of all, thanks for the tool ! I wanted to have your insights on using the tool to screen viruses (bacteriophages) for AMR genes. Best,

evolarjun commented 2 years ago

Hi @conchaeloko,

I haven't used it to screen phage specifically, but assuming you're screening assembled sequence for the phage AMRFinderPlus should identify bacterial AMR genes included in that sequence. Note that to take advantage of the power of the HMM library to identify novel genes not included in the Reference Gene Catalog AMRFinderPlus needs protein sequences.

Let us know how it goes, Arjun

lonestarling commented 2 years ago

Hi, First of all, thanks for the tool ! I wanted to have your insights on using the tool to screen viruses (bacteriophages) for AMR genes. Best,

Hey，guys Have you finished the work about screen viruses (bacteriophages) for AMR genes.？ thanks chen

conchaeloko commented 2 years ago

Hi all, I tried the program on some new phages and it seems like it successfully screened the phages (the results were no AMR genes found). I would like to try it on previously described phages with known AMR genes before relying on the tool.

Best, Robby